tbuckley/cabot-search huggingface dataset:
Embracing sensorimotor history: Time-synchronous and time-unrolled Markov blankets in the free-energy principle
Authors: Nathaniel Virgo, Fernando E. Rosas, Martin Biehl
Journal: Behavioral and Brain Sciences (2022)

Abstract The free-energy principle (FEP) builds on an assumption that sensor–motor loops exhibit Markov blankets in stationary state. We argue that there is rarely reason to assume a system's internal and external states are conditionally independent given the sensorimotor states, and often reason to assume otherwise. However, under mild assumptions internal and external states are conditionally independent given the sensorimotor history .
Squid Suckerin‐Spider Silk Fusion Protein Hydrogel for Delivery of Mesenchymal Stem Cell Secretome to Chronic Wounds
Authors: Kenrick Koh, Jun Kit Wang, James Xiao Yuan Chen, Shu Hui Hiew, Hong Sheng Cheng, Bartosz Gabryelczyk, Marcus Ivan Gerard Vos, Yun Sheng Yip, Liyan Chen, Radoslaw M. Sobota, Damian Kang Keat Chua, Nguan Soon Tan, Chor Yong Tay, Ali Miserez
Journal: Advanced Healthcare Materials (2022)

Chronic wounds are non-healing wounds characterized by a prolonged inflammation phase. Excessive inflammation leads to elevated protease levels and consequently to a decrease in growth factors at wound sites. Stem cell secretome therapy has been identified as a treatment strategy to modulate the microenvironment of chronic wounds via supplementation with anti-inflammatory/growth factors. However, there is a need to develop better secretome delivery systems that are able to encapsulate the secretome without denaturation, in a sustained manner, and that are fully biocompatible. To address this gap, a recombinant squid suckerin-spider silk fusion protein is developed with cell-adhesion motifs capable of thermal gelation at physiological temperatures to form hydrogels for encapsulation and subsequent release of the stem cell secretome. Freeze-thaw treatment of the protein hydrogel results in a modified porous cryogel that maintains slow degradation and sustained secretome release. Chronic wounds of diabetic mice treated with the secretome-laden cryogel display increased wound closure, presence of endothelial cells, granulation wound tissue thickness, and reduced inflammation with no fibrotic scar formation. Overall, these in vivo indicators of wound healing demonstrate that the fusion protein hydrogel displays remarkable potential as a delivery system for secretome-assisted chronic wound healing.
Comparing immunogenicity and efficacy of two different mRNA-based COVID-19 vaccines as a fourth dose; six-month follow-up, Israel, 27 December 2021 to 24 July 2022
Authors: Noam Barda, Michal Canetti, Mayan Gilboa, Victoria Indenboim, Keren Asraf, Yael Weiss-Ottolenghi, Sharon Amit, Daniel Zibly, Ram Doolman, Ella Mendelson, Dror Harats, Laurence S. Freedman, Yitshak Kreiss, Yaniv Lustig, Gili Regev-Yochay
Journal: Eurosurveillance (2022)

We assess the immunogenicity and efficacy of Spikevax and Comirnaty as fourth dose COVID-19 vaccines. Six months post-fourth-dose, IgG levels were higher than pre-fourth dose at 1.58-fold (95% CI: 1.27–1.97) in Spikevax and 1.16-fold (95% CI: 0.98–1.37) in Comirnaty vaccinees. Nearly 60% (159/274) of vaccinees contracted SARS-CoV-2. Infection hazard ratios (HRs) for Spikevax (0.82; 95% CI: 0.62–1.09) and Comirnaty (0.86; 95% CI: 0.65–1.13) vaccinees were similar, as were substantial-disease HRs, i.e. 0.28 (95% CI: 0.13–0.62) and 0.51 (95% CI: 0.27–0.96), respectively.
Consensus-Based Recommendations on Priority Activities to Address Acute Kidney Injury in Children
Authors: Stuart L. Goldstein, Ayse Akcan-Arikan, Rashid Alobaidi, David J. Askenazi, Sean M. Bagshaw, Matthew Barhight, Erin Barreto, Benan Bayrakci, Orville N.R. Bignall, Erica Bjornstad, Patrick D. Brophy, Rahul Chanchlani, Jennifer R. Charlton, Andrea L. Conroy, Akash Deep, Prasad Devarajan, Kristin Dolan, Dana Y. Fuhrman, Katja M. Gist, Stephen M. Gorga, Jason H. Greenberg, Denise Hasson, Emma Heydari Ulrich, Arpana Iyengar, Jennifer G. Jetton, Catherine Krawczeski, Leslie Meigs, Shina Menon, Jolyn Morgan, Catherine J. Morgan, Theresa Mottes, Tara M. Neumayr, Zaccaria Ricci, David Selewski, Danielle E. Soranno, Michelle Starr, Natalja L. Stanski, Scott M. Sutherland, Jordan Symons, Marcelo S. Tavares, Molly Wong Vega, Michael Zappitelli, Claudio Ronco, Ravindra L. Mehta, John Kellum, Marlies Ostermann, Rajit K. Basu
Journal: JAMA Network Open (2022)

Importance Increasing evidence indicates that acute kidney injury (AKI) occurs frequently in children and young adults and is associated with poor short-term and long-term outcomes. Guidance is required to focus efforts related to expansion of pediatric AKI knowledge. Objective To develop expert-driven pediatric specific recommendations on needed AKI research, education, practice, and advocacy. Evidence Review At the 26th Acute Disease Quality Initiative meeting conducted in November 2021 by 47 multiprofessional international experts in general pediatrics, nephrology, and critical care, the panel focused on 6 areas: (1) epidemiology; (2) diagnostics; (3) fluid overload; (4) kidney support therapies; (5) biology, pharmacology, and nutrition; and (6) education and advocacy. An objective scientific review and distillation of literature through September 2021 was performed of (1) epidemiology, (2) risk assessment and diagnosis, (3) fluid assessment, (4) kidney support and extracorporeal therapies, (5) pathobiology, nutrition, and pharmacology, and (6) education and advocacy. Using an established modified Delphi process based on existing data, workgroups derived consensus statements with recommendations. Findings The meeting developed 12 consensus statements and 29 research recommendations. Principal suggestions were to address gaps of knowledge by including data from varying socioeconomic groups, broadening definition of AKI phenotypes, adjudicating fluid balance by disease severity, integrating biopathology of child growth and development, and partnering with families and communities in AKI advocacy. Conclusions and Relevance Existing evidence across observational study supports further efforts to increase knowledge related to AKI in childhood. Significant gaps of knowledge may be addressed by focused efforts.
Selected Bibliography of Recent Research in Chronic Obstructive Pulmonary Disease
Authors: Ashraf Fawzy, Jonathan R. Baker, Thomas L. Keller, Laura C. Feemster, Louise E. Donnelly, Nadia N. Hansel
Journal: American Journal of Respiratory and Critical Care Medicine (2022)

"Selected Bibliography of Recent Research in Chronic Obstructive Pulmonary Disease." American Journal of Respiratory and Critical Care Medicine, 206(11), pp. 1408–1417
Brain-targeted CRISPR/Cas9 nanomedicine for effective glioblastoma therapy
Authors: Weimin Ruan, Mingzhu Jiao, Sen Xu, Muhammad Ismail, Xuan Xie, Yang An, Haixing Guo, Rongjun Qian, Bingyang Shi, Meng Zheng
Journal: Journal of Controlled Release (2022)
Eligibility for Lung Cancer Screening Among Women Receiving Screening for Breast Cancer
Authors: Ashley L. Titan, Ioana Baiu, Doug Liou, Natalie S. Lui, Mark Berry, Joseph Shrager, Leah Backhus
Journal: JAMA Network Open (2022)

Blurb: This cohort study assesses the number of women who were eligible for and underwent lung cancer screening among those who received mammograms at a single academic medical center.
Zwitterionic Polymer/Polydopamine Coating of Electrode Arrays Reduces Fibrosis and Residual Hearing Loss after Cochlear Implantation
Authors: Anning Chen, Dongxiu Chen, Kai Lv, Guowei Li, Jing Pan, Dong Ma, Jie Tang, Hongzheng Zhang
Journal: Advanced Healthcare Materials (2022)

Abstract Since the first surgery 50 years ago, cochlear implantation (CI) is the major treatment for patients with severe sensorineural hearing loss. However, unexpected foreign body reactions (FBRs) after surgery are reported in 90% of CI recipients, resulting in the formation of fibrosis in the cochlea and progressive residual hearing loss. Zwitterion modification is universally used to reduce bio‐fouling and suppress FBRs but never for CI. In the present study, a zwitterionic coating is developed, which is composed of poly sulfobetaine methacrylate (PSB) and polydopamine (PDA) for cochlear implants. The PSB‐PDA coating shows a series of characters for an ideal anti‐FBRs material, including super‐hydrophilicity, low protein and cell adsorption, long‐term stability, and high biocompatibility. Compared to the uncoated controls, PSB‐PDA coating inhibits the activation of macrophages and reduces the release of inflammatory factors (TNF‐ α , IL‐1 β , NO) and fibrosis‐related factors (TGF‐ β 1, α ‐SMA, collagen I). PSB‐PDA coated electrode arrays suppress fibrosis completely and preserve residual hearing significantly in rat CI models. These results suggest that PSB‐PDA coating is a novel strategy for anti‐fibrosis to improve the outcomes of CI.
Markov blankets and Bayesian territories
Authors: Jeff Beck
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg et al. argue that one ought not confuse the map (model) for the territory (reality) and delineate a distinction between innocuous Pearl blankets and metaphysically laden Friston blankets. I argue that all we have are models, all knowledge is conditional, and that if there is a Pearl/Friston distinction, it is a matter of the domain of application: latents or observations. This suggests that, if anything, Friston blankets may inherit philosophical significance previously assigned to observations.
Who tailors the blanket?
Authors: Keisuke Suzuki, Katsunori Miyahara, Kengo Miyazono
Journal: Behavioral and Brain Sciences (2022)

Abstract The gap between the Markov blanket and ontological boundaries arises from the former's inability to capture the dynamic process through which biological and cognitive agents actively generate their own boundaries with the environment. Active inference in the free-energy principle (FEP) framework presupposes the existence of a Markov blanket, but it is not a process that actively generates the latter.
Making life and mind as clear as possible, but not clearer
Authors: Alex Gomez-Marin
Journal: Behavioral and Brain Sciences (2022)

Neuroscience needs theory. Ideas without data are blind, and yet mechanisms without concepts are empty. Friston's free energy principle paradigmatically illustrates the power and pitfalls of current theoretical biology. Mighty metaphors, turned into mathematical models, can become mindless metaphysics. Then, seeking to understand everything in principle, we may explain nothing in practice. Life can't live in a map.
The empire strikes back: Some responses to Bruineberg and colleagues
Authors: Maxwell J. D. Ramstead
Journal: Behavioral and Brain Sciences (2022)

Abstract In their target paper, Bruineberg and colleagues provide us with a timely opportunity to discuss the formal constructs and philosophical implications of the free energy principle. I critically discuss their proposed distinction between Pearl and Friston blankets. I then critically assess the distinction between inference with a model and inference within a model in light of instrumentalist approaches to science.
The map, the territory, and the cartographer: Linking the “pure” formal models to the “murky” material world
Authors: Anna Ciaunica
Journal: Behavioral and Brain Sciences (2022)

Assigning to Pearl blankets an instrumental, a "pure" formal role, tacitly delegates the thorny question of mapping the "murky" territory to empirical sciences. But this move side-lines the problem, and does not offer a solution to the question: How do we relate the formal properties of an agent's model of the world to the real properties of the world itself?
Use of healthcare reimbursement data to monitor bacterial sexually transmitted infection testing in France, 2006 to 2020
Authors: Delphine Viriot, Etienne Lucas, Bertille de Barbeyrac, Cécile Bébéar, Sébastien Fouéré, Nicolas Dupin, Antoine Bertolotti, Béatrice Berçot, Charles Cazanave, Gilles Delmas, Josiane Pillonel, Florence Lot, Ndeindo Ndeikoundam Ngangro
Journal: Eurosurveillance (2022)

BackgroundDiagnoses of bacterial sexually transmitted infections (STIs) have increased in France since the 2000s. The main strategy to control STI transmission is recommending/facilitating access to condom use, testing, and antibiotic treatments.AimThis study analyses the evolution of STI testing in the private sector in France from 2006 to 2020.MethodsNational health insurance reimbursement data were used to determine numbers and rates of individuals aged ≥ 15 years tested for diagnoses of chlamydia, gonorrhoea and syphilis in the private sector in France and to describe their evolution from 2006 to 2020.ResultsUpward tendencies in testing were observed from 2006 to 2019 for all three STIs. The highest testing rates were identified in people aged 25‒29-years old. The observed testing-increase from 2017 to 2019 was twice as high in young people (< 25 years old) as in older people. In 2019, chlamydia, gonorrhoea and syphilis testing rates were respectively 45.4 (+ 21% since 2017), 41.3 (+ 60%), and 47.2 (+ 22%) per 1,000 inhabitants. For all STIs combined, the number of tested individuals decreased by 37% between March and April 2020 during the first COVID-19 epidemic wave and lockdown in France.ConclusionImprovements found in STI testing rates may have resulted from better awareness, especially among young people and health professionals, of the importance of testing, following prevention campaigns. Nevertheless, testing levels remain insufficient considering increasing diagnoses. In 2020, the COVID-19 pandemic had a considerable impact on STI testing. Partner notification and offering diverse testing opportunities including self-sampling are essential to control STI epidemics particularly in exposed populations.
Causal surgery under a Markov blanket
Authors: Daniel Yon, Philip Robert Corlett
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg et al. provide compelling clarity on the roles Markov blankets could (and perhaps should) play in the study of life and mind. However, here we draw attention to a further role blankets might play: as a hypothesis about cognition itself. People and other animals may use blanket-like representations to model the boundary between themselves and their worlds.
Association of Cystatin C Kidney Function Measures With Long-term Deficit-Accumulation Frailty Trajectories and Physical Function Decline
Authors: Chenglong Li, Yanjun Ma, Chao Yang, Rong Hua, Wuxiang Xie, Luxia Zhang
Journal: JAMA Network Open (2022)

It remains unclear whether cystatin C and cystatin C-based kidney function measures are associated with frailty trajectories and physical function decline.
Trends in Enrollment in Employer-Sponsored Health Insurance in the US Before and During the COVID-19 Pandemic, January 2019 to June 2021
Authors: Ravi B. Parikh, Amol S. Navathe, Yueming Zhao, David Pagnotti, Ezekiel J. Emanuel
Journal: JAMA Network Open (2022)

This cross-sectional study compares trends in employer-sponsored health insurance coverage in the US before and during the COVID-19 pandemic.
Against free energy, for direct perception
Authors: Thomas A. Stoffregen, Robert Heath
Journal: Behavioral and Brain Sciences (2022)

We question the free energy principle (FEP) as it is used in contemporary physics. If the FEP is incorrect in physics, then it cannot ground the authors' arguments. We also question the assumption that perception requires inference. We argue that perception (including perception of social affordances) can be direct, in which case inference is not required.
Can high COVID-19 vaccination rates in adults help protect unvaccinated children? Evidence from a unique mass vaccination campaign, Schwaz/Austria, March 2021
Authors: Hannes Winner, Janine Kimpel, Florian Krammer, Dorothee von Laer, Jörg Paetzold
Journal: Eurosurveillance (2022)

Background After an outbreak of the SARS-CoV-2 Beta variant in the district of Schwaz/Austria, vaccination with Comirnaty vaccine (BNT162b2 mRNA, BioNTech-Pfizer) had been offered to all adult inhabitants (≥ 16 years) in March 2021. This made Schwaz one of the most vaccinated regions in Europe at that time (70% of the adult population took up the offer). In contrast, all other Austrian districts remained with low vaccine coverage. Aim We studied whether this rapid mass vaccination campaign provided indirect protection to unvaccinated individuals such as children (&lt; 16 years) living in the same district. Methods To study the effect of the campaign we used two complementary approaches. We compared infection rates among the population of children (&lt; 16 years) in Schwaz with (i) the child population from similar districts (using the synthetic control method), and (ii) with the child population from municipalities along the border of Schwaz not included in the campaign (using an event study approach). Results Before the campaign, we observed very similar infection spread across the cohort of children in Schwaz and the control regions. After the campaign, we found a significant reduction of new cases among children of −64.5% (95%-CI: −82.0 to −30.2%) relative to adjacent border municipalities (using the event study model). Employing the synthetic control method, we observed a significant reduction of −42.8% in the same cohort. Conclusion Our results constitute novel evidence of an indirect protection effect from a group of vaccinated individuals to an unvaccinated group.
Clinicogenomic characteristics and synthetic lethal implications of germline homologous recombination‐deficient hepatocellular carcinoma
Authors: Jihyun An, Ji‐Hye Oh, Bora Oh, Yoo‐Jin Oh, Jin‐Sung Ju, Wonkyung Kim, Hyo Jung Kang, Chang Ohk Sung, Ju Hyun Shim
Journal: Hepatology (2022)

Backgrounds and Aims: We performed an in‐depth examination of pathogenic germline variants (PGVs) and somatic variants in DNA damage response (DDR) genes in hepatocellular carcinoma (HCC) to explore their clinical and genomic impacts. Approach and Results: We used a merged whole‐exome or RNA sequencing data set derived from in‐house ( n = 230) and The Cancer Genome Atlas ( n = 362) databases of multiethnic HCC samples. We also evaluated synthetic lethal approaches targeting mutations in homologous recombination (HR) genes using HCC cells selected from five genomic databases of cancer cell lines. A total of 110 PGVs in DDR pathways in 96 patients were selected. Of the PGV carriers, 44 were HR‐altered and found to be independently associated with poorer disease‐free survival after hepatectomy. The most frequently altered HR gene in both germline and somatic tissues was POLQ , and this variant was detected in 22.7% (10/44) and 23.8% (5/21) of all the corresponding carriers, respectively. PGVs in HR were significantly associated with upregulation of proliferation and replication‐related genes and familial risk of HCC. Samples harboring PGVs in HR with loss of heterozygosity were most strongly correlated with the genomic footprints of deficient HR, such as mutation burden and denovoSig2 (analogous to Catalogue of Somatic Mutations in Cancer [COSMIC] 3), and poor outcome. Pharmacologic experiments with HCC cells defective in BRCA2 or POLQ suggested that tumors with this phenotype are synthetic lethal with poly(ADP‐ribose) polymerase inhibitors. Conclusions: Our findings suggest that germline HR defects in HCC tend to confer a poor prognosis and result in distinctive genomic scarring. Tests of the clinical benefits of HR‐directed treatments in the affected patients are needed.
Life, mind, agency: Why Markov blankets fail the test of evolution
Authors: Walter Veit, Heather Browning
Journal: Behavioral and Brain Sciences (2022)

Abstract There has been much criticism of the idea that Friston's free-energy principle can unite the life and mind sciences. Here, we argue that perhaps the greatest problem for the totalizing ambitions of its proponents is a failure to recognize the importance of evolutionary dynamics and to provide a convincing adaptive story relating free-energy minimization to organismal fitness.
Replacement Fibrosis in the Diaphragm of Mechanically Ventilated Critically Ill Patients
Authors: Zhonghua Shi, Marloes van den Berg, Sylvia Bogaards, Stefan Conijn, Marinus Paul, Albertus Beishuizen, Leo Heunks, Coen A. C. Ottenheijm
Journal: American Journal of Respiratory and Critical Care Medicine (2022)

"Replacement Fibrosis in the Diaphragm of Mechanically Ventilated Critically Ill Patients." American Journal of Respiratory and Critical Care Medicine, 0(ja), pp. –
Good theoretical debate, but insufficient proof of concept
Authors: Rainer Spiegel
Journal: Behavioral and Brain Sciences (2022)

Abstract Bruineberg and colleagues argue that the patellar reflex cannot be modeled sufficiently with a Friston blanket due to counterintuitive sensorimotor boundaries. Although I agree with their theoretical discussion, their model of the patellar reflex is insufficiently based on clinical knowledge. Consequently, this example should not be applied to challenge Friston blankets. I will provide an alternative example.
Trends in Diagnosed Attention-Deficit/Hyperactivity Disorder Among Children, Adolescents, and Adults in Japan From April 2010 to March 2020
Authors: Daimei Sasayama, Rie Kuge, Yuki Toibana, Hideo Honda
Journal: JAMA Network Open (2022)

This cohort study assesses trends in incidence of attention-deficit/hyperactivity disorder (ADHD) among children, adolescents, and adults in Japan from 2010 to 2019.
Delayed type hypersensitivity reactions to various allergens may differently model inflammatory skin diseases
Authors: Ana B. Pavel, Ester Del Duca, Julia Cheng, Jianni Wu, Benjamin Ungar, Yeriel D. Estrada, Carolyn Jack, Catherine Maari, Étienne Saint‐Cyr Proulx, Francisco Ramirez‐Valle, James G. Krueger, Robert Bissonnette, Emma Guttman‐Yassky
Journal: Allergy (2022)

Abstract Background Treatment of inflammatory skin diseases, including atopic dermatitis (AD) and psoriasis, is undergoing transformative changes, highlighting the need to develop experimental models of skin inflammation in humans to predict treatment responses. Methods We topically or intradermally administered four common sensitizers (dust mite (DM), diphencyprone (DPCP), nickel (Ni), and purified protein derivative (PPD)) to the backs of 40 healthy patients and the skin hypersensitivity response was biopsied and evaluated using immunohistochemistry, RNA‐seq, and RT‐PCR. Results All agents induced strong increases in cellular infiltrates (T‐cells and dendritic cells) as compared to untreated skin ( p &lt; .05), with variable T helper polarization. Overall, DPCP induced the strongest immune responses across all pathways, including innate immunity (IL‐1α, IL‐8), Th1 (IFNγ, CXCL10), Th2 (IL‐5, CCL11), and Th17 (CAMP/LL37) products, as well as the highest regulatory tone (FOXP3, IL‐34, IL‐37) (FDR &lt;0.01). Nickel induced Th17 (IL‐17A), Th1 (CXCL10) and Th2 (IL‐4R) immune responses to a lesser extent than DPCP ( p &lt; .05). PPD induced predominantly Th1 (IFNγ, CXCL10, STAT1) and Th17 inflammation (IL‐17A) ( p &lt; .05). DM induced modulation of Th2 (IL‐13, CCL17, CCL18), Th22 (IL‐22), and Th17/Th22 (S100A7/9/12) pathways ( p &lt; .05). Barrier defects that characterize both AD and psoriasis were best modeled by DPCP and Ni, followed by PPD, including downregulation of terminal differentiation (FLG, FLG2, LOR, LCEs), tight junction (CLDN1/CLDN8), and lipid metabolism (FA2H, FABP7)‐related markers. Conclusion Our data imply that DPCP induced the strongest immune response across all pathways, and barrier defects characteristic of AD and psoriasis.
The seductive allure of cargo cult computationalism
Authors: Micah Allen
Journal: Behavioral and Brain Sciences (2022)

Bruineberg and colleagues report a striking confusion, in which the formal Bayesian notion of a "Markov blanket" has been frequently misunderstood and misapplied to phenomena of mind and life. I argue that misappropriation of formal concepts is pervasive in the "predictive processing" literature, and echo Richard Feynman in suggesting how we might resist the allure of cargo cult computationalism.